Hi Pengfei.
I sent email with .prmtop file.
But I received this email moderator AMBER list.
"...
our mail to 'AMBER' with the subject
Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II)
Is being held until the list moderator can review it for approval.
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How to send your file to try to add the term C4?
Regards,
Marcelo
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2015-10-22 18:58 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Marcelo,
>
> Actually you can add C4 to two types of metal by using add12_6_4 command
> in ParmEd. In that case you need to use one ambermask to represent the two
> ions in the command line. But there may be some bugs in the former code and
> I am not sure the updates of AmberTools15 have fixed it or not. You can
> also send me the topology file for adding C4 term and I can help to add the
> C4 terms for you.
>
> Are you going to investigate the ligand exchange in the coordination
> shell? If not, you can also try to build the bonded model using MCPB.py,
> here is the related tutorial:
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
>
> Best,
> Pengfei
>
> > On Oct 22, 2015, at 3:24 PM, Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com> wrote:
> >
> > Hi Pengfei,
> >
> > I was thinking here, and I began to doubt what made so far in this case.
> >
> > I guess my first question should have acid: you can enter the term C4
> > the ion model is not connected 04/06/12-LJ for a system that has the
> active
> > site
> > a metallic center type (Fe (III) -M (II)?
> >
> > Was studying the model again in A20 tutorial and it seems to me only
> > One can add the term C4 to active sites with only one type of metal.
> >
> > It concludes that correct?
> >
> > Best regards,
> >
> > Marcelo
> >
> > Marcelo Andrade Chagas, MSc
> > (PhD student)
> > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> > * http://lqcmm.qui.ufmg.br/
> > Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> > Tel:(31)3409-5776
> >
> > 2015-10-22 12:36 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> >
> >> Hi Marcelo,
> >>
> >> What residues coordinate to the Fe(III) and Zn(II) ions?
> >>
> >> Best,
> >> Pengfei
> >>
> >>> On Oct 22, 2015, at 10:34 AM, Marcelo Andrade Chagas <
> >> andrade.mchagas.gmail.com> wrote:
> >>>
> >>> Dear AMBER of the list,
> >>>
> >>> How to use unbound ion model described in the tutorial:
> >>>
> >>> 12-6-4 LJ-type nonbonded model in the AMBER,
> >>>
> >>> to systems like proteins Fe(III)-M(II) ...M=Zn(II)?
> >>>
> >>> Best regards,
> >>>
> >>> Marcelo
> >>>
> >>> Marcelo Andrade Chagas, MSc
> >>> (PhD student)
> >>> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> >>> * http://lqcmm.qui.ufmg.br/
> >>> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> >>> Tel:(31)3409-5776
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 23 2015 - 16:00:03 PDT
